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Input form  |  Web services  |  Help & Documentation  |  Bioinformatics Tools FAQ

Introduction

BLAST stands for Basic Local Alignment Search Tool.The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your sequence.

Official Website

NCBI BLAST website

Download Software

FTP Download

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...) (See example input formats)
  • In the following steps, the user has the possibility to change the default tool parameters (See example output formats)
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Database

Databases

Database

Database NameDescriptionAbbreviation
ENA Sequence (formerly EMBL-Bank)ENA Sequence (formerly EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.
ENA Sequence ReleaseThe quarterly release of the ENA Sequenceem_rel
 ENA Sequence EnvironmentalSequences from Environmental Samples.em_rel_env
  ENA Sequence EST Environmental
em_rel_est_env
  ENA Sequence GSS Environmental
em_rel_gss_env
  ENA Sequence HTC Environmental
em_rel_htc_env
  ENA Sequence HTG Environmental
em_rel_htg_env
  ENA Sequence Patent Environmental
em_rel_pat_env
  ENA Sequence Standard Environmental
em_rel_std_env
  ENA Sequence STS Environmental
em_rel_sts_env
  ENA Sequence TSA Environmental
em_rel_tsa_env
 ENA Sequence FungiSequences from Fungi.em_rel_fun
  ENA Sequence EST Fungi
em_rel_est_fun
  ENA Sequence GSS Fungi
em_rel_gss_fun
  ENA Sequence HTC Fungi
em_rel_htc_fun
  ENA Sequence HTG Fungi
em_rel_htg_fun
  ENA Sequence Patent Fungi
em_rel_pat_fun
  ENA Sequence Standard Fungi
em_rel_std_fun
  ENA Sequence STS Fungi
em_rel_sts_fun
  ENA Sequence TSA Fungi
em_rel_tsa_fun
 ENA Sequence HumanSequences from Human.em_rel_hum
  ENA Sequence EST Human
em_rel_est_hum
  ENA Sequence GSS Human
em_rel_gss_hum
  ENA Sequence HTC Human
em_rel_htc_hum
  ENA Sequence HTG Human
em_rel_htg_hum
  ENA Sequence Patent Human
em_rel_pat_hum
  ENA Sequence Standard Human
em_rel_std_hum
  ENA Sequence STS Human
em_rel_sts_hum
 ENA Sequence InvertebrateSequences from invertebrate organisms.em_rel_inv
  ENA Sequence EST Invertebrate
em_rel_est_inv
  ENA Sequence GSS Invertebrate
em_rel_gss_inv
  ENA Sequence HTC Invertebrate
em_rel_htc_inv
  ENA Sequence HTG Invertebrate
em_rel_htg_inv
  ENA Sequence Patent Invertebrate
em_rel_pat_inv
  ENA Sequence Standard Invertebrate
em_rel_std_inv
  ENA Sequence STS Invertebrate
em_rel_sts_inv
  ENA Sequence TSA Invertebrate
em_rel_tsa_inv
 ENA Sequence MammalSequences from mammals, excluding rodents and humans.em_rel_mam
  ENA Sequence EST Mammal
em_rel_est_mam
  ENA Sequence GSS Mammal
em_rel_gss_mam
  ENA Sequence HTC Mammal
em_rel_htc_mam
  ENA Sequence HTG Mammal
em_rel_htg_mam
  ENA Sequence Patent Mammal
em_rel_pat_mam
  ENA Sequence Standard Mammal
em_rel_std_mam
  ENA Sequence STS Mammal
em_rel_sts_mam
  ENA Sequence TSA Mammal
em_rel_tsa_mam
 ENA Sequence MouseSequences from mus musculus.em_rel_mus
  ENA Sequence EST Mouse
em_rel_est_mus
  ENA Sequence GSS Mouse
em_rel_gss_mus
  ENA Sequence HTC Mouse
em_rel_htc_mus
  ENA Sequence HTG Mouse
em_rel_htg_mus
  ENA Sequence Patent Mouse
em_rel_pat_mus
  ENA Sequence Standard Mouse
em_rel_std_mus
  ENA Sequence STS Mouse
em_rel_sts_mus
 ENA Sequence PhageSequences from bacteria phages.em_rel_phg
  ENA Sequence GSS Phage
em_rel_gss_phg
  ENA Sequence HTG Phage
em_rel_htg_phg
  ENA Sequence Patent Phage
em_rel_pat_phg
  ENA Sequence Standard Phage
em_rel_std_phg
 ENA Sequence PlantSequences from plants.em_rel_pln
  ENA Sequence EST Plant
em_rel_est_pln
  ENA Sequence GSS Plant
em_rel_gss_pln
  ENA Sequence HTC Plant
em_rel_htc_pln
  ENA Sequence HTG Plant
em_rel_htg_pln
  ENA Sequence Patent Plant
em_rel_pat_pln
  ENA Sequence Standard Plant
em_rel_std_pln
  ENA Sequence STS Plant
em_rel_sts_pln
  ENA Sequence TSA Plant
em_rel_tsa_pln
 ENA Sequence ProkaryoteSequences from prokaryotes.em_rel_pro
  ENA Sequence EST Prokaryote
em_rel_est_pro
  ENA Sequence GSS Prokaryote
em_rel_gss_pro
  ENA Sequence HTC Prokaryote
em_rel_htc_pro
  ENA Sequence HTG Prokaryote
em_rel_htg_pro
  ENA Sequence Patent Prokaryote
em_rel_pat_pro
  ENA Sequence Standard Prokaryote
em_rel_std_pro
  ENA Sequence STS Prokaryote
em_rel_sts_pro
  ENA Sequence TSA Prokaryote
em_rel_tsa_pro
 ENA Sequence RodentSequences from rodents, but not mouse.em_rel_rod
  ENA Sequence EST Rodent
em_rel_est_rod
  ENA Sequence GSS Rodent
em_rel_gss_rod
  ENA Sequence HTC Rodent
em_rel_htc_rod
  ENA Sequence HTG Rodent
em_rel_htg_rod
  ENA Sequence Patent Rodent
em_rel_pat_rod
  ENA Sequence Standard Rodent
em_rel_std_rod
  ENA Sequence STS Rodent
em_rel_sts_rod
  ENA Sequence TSA Rodent
em_rel_tsa_rod
 ENA Sequence SyntheticSequences from synthetic constructs.em_rel_syn
  ENA Sequence Patent Synthetic
em_rel_pat_syn
  ENA Sequence Standard Synthetic
em_rel_std_syn
 ENA Sequence TransgenicSequences from transgenic contructs.em_rel_tgn
  ENA Sequence Standard Transgenic
em_rel_std_tgn
  ENA Sequence GSS Transgenic
em_rel_gss_tgn
 ENA Sequence UnclassifiedSequences from unspecified origin.em_rel_unc
  ENA Sequence EST Unclassified
em_rel_est_unc
  ENA Sequence Patent Unclassified
em_rel_pat_unc
  ENA Sequence Standard Unclassified
em_rel_std_unc
 ENA Sequence ViralSequences from Viruses.em_rel_vrl
  ENA Sequence EST Viral
em_rel_est_vrl
  ENA Sequence GSS Viral
em_rel_gss_vrl
  ENA Sequence HTG Viral
em_rel_htg_vrl
  ENA Sequence Patent Viral
em_rel_pat_vrl
  ENA Sequence Standard Viral
em_rel_std_vrl
  ENA Sequence TSA Viral
em_rel_tsa_vrl
 ENA Sequence VertebrateSequences from vertebrates, excluding human, mouse and rodents.em_rel_vrt
  ENA Sequence EST Vertebrate
em_rel_est_vrt
  ENA Sequence GSS Vertebrate
em_rel_gss_vrt
  ENA Sequence HTC Vertebrate
em_rel_htc_vrt
  ENA Sequence HTG Vertebrate
em_rel_htg_vrt
  ENA Sequence Patent Vertebrate
em_rel_pat_vrt
  ENA Sequence Standard Vertebrate
em_rel_std_vrt
  ENA Sequence STS Vertebrate
em_rel_sts_vrt
  ENA Sequence TSA Vertebrate
em_rel_tsa_vrt
ENA Sequence UpdatesDaily updates to the quarterly ENA Sequence releaseemnew
ENA Coding Sequence ReleaseThe nucleotide sequences of the ENA Coding Sequence Release.em_cds_rel
ENA Coding Sequence UpdatesThe nucleotide sequences of the ENA Coding Sequence Updates.em_cds_cum
ENA Non-Coding Sequence ReleaseThe nucleotide sequences of the ENA Coding Sequence Release.em_ncr_rel
ENA Non-Coding Sequence UpdatesThe nucleotide sequences of the ENA Non-Coding Sequence Updates.em_ncr_cum
ENA Geospatial ReleaseThe nucleotide sequences of the ENA Geospatial Sequence Release.em_geo_rel
ENA Geospatial UpdatesThe nucleotide sequences of the ENA Geospatial Sequence Updates.em_geo_cum
Others

 ENA Sequence Expressed Sequence Tag
em_rel_est
 ENA Sequence Genome Survey Sequence
em_rel_gss
 ENA Sequence High Throughput cDNA
em_rel_htc
 ENA Sequence High Throughput Genome
em_rel_htg
 ENA Sequence Patent
em_rel_pat
 ENA Sequence Standard
em_rel_std
 ENA Sequence Sequence Tagged Site
em_rel_sts
 ENA Sequence Transcriptome Shotgun Assembly
em_rel_tsa
 ENA Sequence Release and Updates
emall
 ENA Sequence VectorsSequencing vectors extracted from the ENA Sequenceemvec
IMGT

IMGT/LIGM-DBThe immunoglobulins and T cell receptors (LIGM-DB) section of the international immunogenetics (IMGT) databaseimgtligm
IMGT/HLAThe human major histocompatibility complex (HLA) section of the the international immunogenetics (IMGT) databaseimgthla
IPD-KIRHuman Killer-cell Immunoglobulin-like Receptors (KIR) sequence in the Immuno Polymorphism Database (IPD)ipdkir
IPD-MHCMajor Histocompatibility Complex (MHC) section of the Immuno Polymorphism Database (IPD)ipdmhc
Patents

NR Patent DNAs Level-1Non-redundant Patent DNAs sequences Level 1 covering patent data from the ENA Sequencenrnl1
NR Patent DNAs Level-2Non-redundant Patent DNAs sequences Level 2 covering patent data from the ENA Sequencenrnl2
Structure

Nucleotide Structure SequencesNucleotide sequences from structures described in the Brookhaven Protein Data Bank(PDB)pdbna

Default value is: ENA Sequence TSA Vertebrate [em_rel_tsa_vrt]

Step 2 - Sequence

Sequence Input Window

The query sequence can be entered directly into this form. The sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing a valid sequence in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be used as input for the sequence similarity search. Word processors files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.

Sequence Type

Indicates if the sequence is protein or DNA/RNA.

TypeAbbreviation
PROTEINprotein
DNA/RNAdna

Default value is: DNA/RNA [dna]

Step 3 - Parameters

Program

The BLAST program to be used for the Sequence Similarity Search.

Program NameDescriptionAbbreviation
blastnCompares a nucleotide sequence (DNA/RNA) to a nucleotide sequence databaseblastn
tblastxCompares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that TBLASTX is extremely slow and cpu-intensive.tblastx
tblastnCompares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.tblastn

Default value is: blastn

Task

Task option (only selectable for blastn)

Task NameDescriptionAbbreviation
blastnTraditional BLASTN taskblastn
megablastMegablast task for quickly searching very similar (e.g., intraspecies or closely related species) sequencesmegablast

Default value is: blastn

Matrix

(Protein searches) The substitution matrix used for scoring alignments when searching the database.

Matrix NameAbbreviation
BLOSUM45BLOSUM45
BLOSUM50BLOSUM50
BLOSUM62BLOSUM62
BLOSUM80BLOSUM80
BLOSUM90BLOSUM90
PAM30PAM30
PAM70PAM70
PAM250PAM250

Default value is: BLOSUM62

Additional informationRead more about matrices

Match/mismatch_scores

(Nucleotide searches) The match score is the bonus to the alignment score when matching the same base. The mismatch is the penalty when failing to match.

Match/mismatch_scores NameAbbreviation
1,-41,-4
2,-72,-7
1,-31,-3
2,-52,-5
1,-21,-2
2,-32,-3
1,-11,-1
5,-45,-4
4,-54,-5

Default value is: 1,-3

Gap Open Penalty

Penalty taken away from the score when a gap is created in sequence. Increasing the gap openning penalty will decrease the number of gaps in the final alignment.

Default value is: default [-1]

Additional informationRead more about gap penalties

Gap Extend Penalty

Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favors short gaps in the final alignment, conversly decreasing the gap extension penalty favors long gaps in the final alignment.

Default value is: default [-1]

Additional informationRead more about gap penalties

Gap Align

This is a true/false setting that tells the program the perform optimised alignments within regions involving gaps. If set to true, the program will perform an alignment using gaps. Otherwise, if it is set to false, it will report only individual HSP where two sequence match each other, and thus will not produce alignments with gaps.

Default value is: true

Additional informationRead more about gap penalties

Expectation Threshold

Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.

Default value is: 10 (default) [10]

Filter

Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.

Default value is: yes [T]

Dropoff

The amount a score can drop before gapped extension of word hits is halted

Default value is: 0 (default) [0]

Scores

Maximum number of match score summaries reported in the result output.

Default value is: 50 (default) [50]

Alignments

Maximum number of match alignments reported in the result output.

Default value is: 50 (default) [50]

Sequence Range

Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell BLAST to only use residues 34 to 89, inclusive.

Default value is: START-END

Alignment Views

Formating for the alignments

NameDescriptionValue
pairwiseThe query and match are output as a pairwsie alignment with a consensus line between the two sequences. In the consensus the match states are represented as: identical match as the base/residue, similarity as a '+' and missmatch as a space.0
Query-anchored identitiesThe matches found are shown relative to the ungapped query sequence as a differences to the query. Identities appear as dots (.), similarites in upper case, missmatches in lower case and gaps as dash (-). Insertions are indictated with a line pointing to the insertion site with the inserted sequence on another line.1
Query-anchored non-identitiesThe matches found are shown relative to the ungapped query sequence as a differences to the query. Identities and similarites appear in upper case, missmatches in lower case and gaps as dash (-). Insertions are indictated with a line pointing to the insertion site with the inserted sequence on another line.2
Flat query-anchored identitiesThe matches found are shown relative to the gapped query sequence as a differences to the query. Identities appear as dots (.), similarites in upper case, missmatches in lower case and gaps as dash (-).3
Flat query-anchored non-identitiesThe matches found are shown relative to the gapped query sequence as a differences to the query. Identities and similarites appear in upper case, missmatches in lower case and gaps as dash (-).4
BLASTXMLOutput NCBI BLAST XML instead of a plain text report.5
tabularSummary output in tabular format.6
tabular with comment linesSummary output in tabular format.7
Text ASN.1Output in ASN.1 format.8
Binary ASN.1Output in ASN.1 format.9
Comma-separated valuesSummary output as comma separated values.10
BLAST archive format (ASN.1)Output in BLAST archive format (ASN.1).11

Default value is: pairwise [0]

Composition-based Statistics

Use composition-based statistics.

NameDescriptionValue
F (default)No composition-based statisticsF
D(equivalent to 2)D
1Composition-based statistics as in NAR 29:2994-3005, 20011
2Composition-based score adjustment as in Bioinformatics 21:902-911,2005, conditioned on sequence properties2
3Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally3

Default value is: F (default) [F]

Translation Table

Query Genetic code to use in translation

NameValue
N/A-1
Standard SGC01
Vertebrate Mitochondrial2
Yeast Mitochondrial3
Mold Mitochondrial Protozoan Mitochondrial Coelenterate4
Invertebrate Mitochondrial5
Ciliate Nuclear Dasycladacean Nuclear Hexamita Nuclear6
Echinoderm Mitochondrial Flatworm Mitochondrial9
Euplotid Nuclear10
Bacterial and Plant Plastid11
Alternative Yeast Nuclear12
Ascidian Mitochondrial13
Alternative Flatworm Mitochondrial14
Blepharisma Macronuclear15
Chlorophycean Mitochondrial16
Trematode Mitochondrial21
Scenedesmus obliquus Mitochondrial22
Thraustochytrium Mitochondrial23

Default value is: Standard SGC0 [1]

Step 4 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

References

BLAST+: architecture and applications.
(2009 December 15) BMC bioinformatics 10 :421
PMID: 20003500Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
(1997 September 01) Nucleic acids research 25 (17) :3389-3402
PMID: 9254694Basic local alignment search tool.
(1990 October 01) Journal of molecular biology 215 (3) :403-410
PMID: 2231712The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
PMID: 25845596Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600
PMID: 23671338

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